Multiple sequence alignment - TraesCS1B01G325600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G325600 chr1B 100.000 2927 0 0 1 2927 551220653 551217727 0.000000e+00 5406.0
1 TraesCS1B01G325600 chr1B 96.111 540 20 1 1 539 551210326 551210865 0.000000e+00 880.0
2 TraesCS1B01G325600 chr7B 94.644 1251 67 0 536 1786 34221072 34222322 0.000000e+00 1940.0
3 TraesCS1B01G325600 chr7B 90.576 1146 99 8 1787 2927 552615120 552613979 0.000000e+00 1509.0
4 TraesCS1B01G325600 chr7B 77.912 1159 204 35 647 1786 571591359 571592484 0.000000e+00 675.0
5 TraesCS1B01G325600 chr7B 96.164 391 13 1 151 539 34225592 34225202 3.180000e-179 638.0
6 TraesCS1B01G325600 chr7B 90.244 164 15 1 9 172 34230875 34230713 2.290000e-51 213.0
7 TraesCS1B01G325600 chr6B 94.968 1093 54 1 536 1628 666827648 666826557 0.000000e+00 1712.0
8 TraesCS1B01G325600 chr6B 90.917 1145 97 5 1787 2927 148069745 148070886 0.000000e+00 1531.0
9 TraesCS1B01G325600 chr6B 89.878 1146 108 7 1783 2922 113468235 113469378 0.000000e+00 1467.0
10 TraesCS1B01G325600 chr6B 89.451 1147 115 6 1782 2923 550215751 550216896 0.000000e+00 1443.0
11 TraesCS1B01G325600 chr6B 95.933 541 20 1 1 539 666793303 666793843 0.000000e+00 876.0
12 TraesCS1B01G325600 chr6B 82.741 985 152 15 540 1518 63423795 63422823 0.000000e+00 861.0
13 TraesCS1B01G325600 chr6B 93.865 163 10 0 1624 1786 666804139 666803977 2.250000e-61 246.0
14 TraesCS1B01G325600 chr6B 83.568 213 35 0 1574 1786 63422824 63422612 1.780000e-47 200.0
15 TraesCS1B01G325600 chr5B 92.112 1141 89 1 1787 2927 698498053 698499192 0.000000e+00 1607.0
16 TraesCS1B01G325600 chr5B 91.652 1114 91 1 1814 2927 424026652 424027763 0.000000e+00 1541.0
17 TraesCS1B01G325600 chr5B 90.576 1146 104 4 1785 2927 378479138 378477994 0.000000e+00 1515.0
18 TraesCS1B01G325600 chr4B 89.921 1141 107 6 1790 2927 589892743 589891608 0.000000e+00 1463.0
19 TraesCS1B01G325600 chr4B 82.538 985 154 17 540 1518 67559116 67558144 0.000000e+00 850.0
20 TraesCS1B01G325600 chr4B 82.629 213 37 0 1574 1786 67558145 67557933 3.850000e-44 189.0
21 TraesCS1B01G325600 chr2B 89.634 1148 110 9 1783 2925 109615791 109616934 0.000000e+00 1452.0
22 TraesCS1B01G325600 chr7D 96.278 618 23 0 1169 1786 2487318 2486701 0.000000e+00 1014.0
23 TraesCS1B01G325600 chr7D 82.389 988 144 19 537 1518 52090177 52091140 0.000000e+00 833.0
24 TraesCS1B01G325600 chr7D 96.659 419 10 4 124 539 2480298 2480715 0.000000e+00 693.0
25 TraesCS1B01G325600 chr7D 82.160 213 38 0 1574 1786 52091139 52091351 1.790000e-42 183.0
26 TraesCS1B01G325600 chr7D 96.341 82 3 0 1 82 2480146 2480227 5.090000e-28 135.0
27 TraesCS1B01G325600 chr7D 95.745 47 2 0 134 180 2480258 2480304 3.130000e-10 76.8
28 TraesCS1B01G325600 chr6D 83.367 986 143 18 540 1518 469087324 469086353 0.000000e+00 893.0
29 TraesCS1B01G325600 chr6D 83.568 213 35 0 1574 1786 469086354 469086142 1.780000e-47 200.0
30 TraesCS1B01G325600 chr3D 82.204 989 145 20 536 1518 496843069 496842106 0.000000e+00 822.0
31 TraesCS1B01G325600 chr3D 84.038 213 34 0 1574 1786 496842107 496841895 3.820000e-49 206.0
32 TraesCS1B01G325600 chr4A 77.912 1159 204 35 647 1786 690106441 690105316 0.000000e+00 675.0
33 TraesCS1B01G325600 chr3B 78.201 867 167 18 703 1561 52925005 52925857 4.290000e-148 534.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G325600 chr1B 551217727 551220653 2926 True 5406.0 5406 100.000000 1 2927 1 chr1B.!!$R1 2926
1 TraesCS1B01G325600 chr1B 551210326 551210865 539 False 880.0 880 96.111000 1 539 1 chr1B.!!$F1 538
2 TraesCS1B01G325600 chr7B 34221072 34222322 1250 False 1940.0 1940 94.644000 536 1786 1 chr7B.!!$F1 1250
3 TraesCS1B01G325600 chr7B 552613979 552615120 1141 True 1509.0 1509 90.576000 1787 2927 1 chr7B.!!$R3 1140
4 TraesCS1B01G325600 chr7B 571591359 571592484 1125 False 675.0 675 77.912000 647 1786 1 chr7B.!!$F2 1139
5 TraesCS1B01G325600 chr6B 666826557 666827648 1091 True 1712.0 1712 94.968000 536 1628 1 chr6B.!!$R2 1092
6 TraesCS1B01G325600 chr6B 148069745 148070886 1141 False 1531.0 1531 90.917000 1787 2927 1 chr6B.!!$F2 1140
7 TraesCS1B01G325600 chr6B 113468235 113469378 1143 False 1467.0 1467 89.878000 1783 2922 1 chr6B.!!$F1 1139
8 TraesCS1B01G325600 chr6B 550215751 550216896 1145 False 1443.0 1443 89.451000 1782 2923 1 chr6B.!!$F3 1141
9 TraesCS1B01G325600 chr6B 666793303 666793843 540 False 876.0 876 95.933000 1 539 1 chr6B.!!$F4 538
10 TraesCS1B01G325600 chr6B 63422612 63423795 1183 True 530.5 861 83.154500 540 1786 2 chr6B.!!$R3 1246
11 TraesCS1B01G325600 chr5B 698498053 698499192 1139 False 1607.0 1607 92.112000 1787 2927 1 chr5B.!!$F2 1140
12 TraesCS1B01G325600 chr5B 424026652 424027763 1111 False 1541.0 1541 91.652000 1814 2927 1 chr5B.!!$F1 1113
13 TraesCS1B01G325600 chr5B 378477994 378479138 1144 True 1515.0 1515 90.576000 1785 2927 1 chr5B.!!$R1 1142
14 TraesCS1B01G325600 chr4B 589891608 589892743 1135 True 1463.0 1463 89.921000 1790 2927 1 chr4B.!!$R1 1137
15 TraesCS1B01G325600 chr4B 67557933 67559116 1183 True 519.5 850 82.583500 540 1786 2 chr4B.!!$R2 1246
16 TraesCS1B01G325600 chr2B 109615791 109616934 1143 False 1452.0 1452 89.634000 1783 2925 1 chr2B.!!$F1 1142
17 TraesCS1B01G325600 chr7D 2486701 2487318 617 True 1014.0 1014 96.278000 1169 1786 1 chr7D.!!$R1 617
18 TraesCS1B01G325600 chr7D 52090177 52091351 1174 False 508.0 833 82.274500 537 1786 2 chr7D.!!$F2 1249
19 TraesCS1B01G325600 chr7D 2480146 2480715 569 False 301.6 693 96.248333 1 539 3 chr7D.!!$F1 538
20 TraesCS1B01G325600 chr6D 469086142 469087324 1182 True 546.5 893 83.467500 540 1786 2 chr6D.!!$R1 1246
21 TraesCS1B01G325600 chr3D 496841895 496843069 1174 True 514.0 822 83.121000 536 1786 2 chr3D.!!$R1 1250
22 TraesCS1B01G325600 chr4A 690105316 690106441 1125 True 675.0 675 77.912000 647 1786 1 chr4A.!!$R1 1139
23 TraesCS1B01G325600 chr3B 52925005 52925857 852 False 534.0 534 78.201000 703 1561 1 chr3B.!!$F1 858

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
607 664 0.46546 GCCAACTGGACTGGTTGTGA 60.465 55.0 0.0 0.0 41.47 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2512 0.036732 TGAAGGTGCAGAAGCCGATT 59.963 50.0 0.0 0.0 41.13 3.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.289834 CAGAGAAATGGAGCAGAGATTGTAT 58.710 40.000 0.00 0.00 0.00 2.29
44 45 4.412796 TGGAGCAGAGATTGTATTGAGG 57.587 45.455 0.00 0.00 0.00 3.86
149 201 8.706492 ATTGTGTGTTTTTATGGCATTATCAG 57.294 30.769 4.78 0.00 0.00 2.90
514 570 8.091449 CCACTTGACAAGAGAAGTATCTAGTTT 58.909 37.037 21.95 0.00 35.54 2.66
607 664 0.465460 GCCAACTGGACTGGTTGTGA 60.465 55.000 0.00 0.00 41.47 3.58
629 686 1.000955 CCTCGTAGGGCGCTCATAAAT 59.999 52.381 11.40 0.00 41.07 1.40
634 691 0.773644 AGGGCGCTCATAAATCCCAT 59.226 50.000 11.40 0.00 39.42 4.00
638 695 2.221169 GCGCTCATAAATCCCATCACA 58.779 47.619 0.00 0.00 0.00 3.58
741 816 0.602638 TCGTGGTGGTTGATCACTGC 60.603 55.000 0.00 0.00 37.75 4.40
784 859 1.003545 CGGCAGAAATCGCTGGTAATG 60.004 52.381 0.00 0.00 36.41 1.90
798 873 1.133761 GGTAATGCCCTTCCTCCTTCC 60.134 57.143 0.00 0.00 0.00 3.46
817 892 1.214367 CGTGCGTCTTGTGGTAGTTT 58.786 50.000 0.00 0.00 0.00 2.66
854 931 4.403113 TGGTTGTCTTTGGTTAGGGTTTTC 59.597 41.667 0.00 0.00 0.00 2.29
880 958 7.255346 CGAGTAGGAAAATTTGTGGTTTTAGGT 60.255 37.037 0.00 0.00 0.00 3.08
886 964 8.609176 GGAAAATTTGTGGTTTTAGGTCTTTTC 58.391 33.333 0.00 0.00 0.00 2.29
924 1002 5.725325 TTGGATTTGATCTTGCATTCACA 57.275 34.783 0.00 0.00 0.00 3.58
928 1006 5.449588 GGATTTGATCTTGCATTCACATCGT 60.450 40.000 11.60 0.00 32.39 3.73
1066 1145 5.395214 GGTCAATTTATTCGAATTGGGCCTT 60.395 40.000 17.19 0.00 43.74 4.35
1107 1186 4.070716 GGGATGAGGCAATGTTAGAGATG 58.929 47.826 0.00 0.00 0.00 2.90
1151 1230 4.142160 GCCAGAAGTGAAAGGTTTTCTTGT 60.142 41.667 3.53 0.00 35.55 3.16
1318 1397 6.183360 GGTTTATGTGGAATATTTTGGGGAGG 60.183 42.308 0.00 0.00 0.00 4.30
1355 1434 3.929610 GCAAGTGATAGTGGAAGTGACTC 59.070 47.826 0.00 0.00 0.00 3.36
1397 1476 2.243478 AGGTAGCAGGAGAGAGTGATGA 59.757 50.000 0.00 0.00 0.00 2.92
1526 1605 7.880713 TGGTGTTATTACTCAAGTGATTAGCAA 59.119 33.333 0.00 0.00 0.00 3.91
1532 1611 5.700402 ACTCAAGTGATTAGCAACCCTAT 57.300 39.130 0.00 0.00 0.00 2.57
1666 1769 2.025887 GGATCACAAAGTGGGAGTGGAT 60.026 50.000 0.00 0.00 30.64 3.41
1679 1782 2.093288 GGAGTGGATCAGCTCATCAACA 60.093 50.000 7.95 0.00 29.87 3.33
1696 1799 8.750515 TCATCAACAAATTATCCATCAGCTAA 57.249 30.769 0.00 0.00 0.00 3.09
1706 1809 5.644977 ATCCATCAGCTAAATCATGCATG 57.355 39.130 21.07 21.07 0.00 4.06
1763 1866 5.843673 TCAGACAGTGAGGAAGATGATAC 57.156 43.478 0.00 0.00 0.00 2.24
2025 2134 6.852853 GCCTATGATTATGATTGTTGTTGTCG 59.147 38.462 0.00 0.00 0.00 4.35
2090 2200 2.908351 AGGGTTACACAAGGTCGGTTAT 59.092 45.455 0.00 0.00 0.00 1.89
2124 2235 7.721399 GGAATCTACATATCCAAATCACCAAGT 59.279 37.037 0.00 0.00 33.30 3.16
2128 2239 6.916360 ACATATCCAAATCACCAAGTTTGT 57.084 33.333 0.00 0.00 34.37 2.83
2133 2244 4.952957 TCCAAATCACCAAGTTTGTCTTCA 59.047 37.500 0.00 0.00 34.37 3.02
2155 2266 1.794714 GCCAAGGAGAGTCCCATCTA 58.205 55.000 0.00 0.00 37.19 1.98
2195 2306 8.802267 GTCTTCTATCTTGTATCTTCATAGCCT 58.198 37.037 0.00 0.00 0.00 4.58
2252 2364 2.206223 GGACCCCTTAATCCAGGACTT 58.794 52.381 0.00 0.00 35.71 3.01
2398 2512 3.325870 CTTTCCACTTGATGTCACGCTA 58.674 45.455 0.00 0.00 0.00 4.26
2520 2636 4.803253 GCCTATTTAAAGAGACGGGGATCC 60.803 50.000 11.41 1.92 0.00 3.36
2675 2791 2.369203 TGTTCTGTATCCCACGGTCAAA 59.631 45.455 0.00 0.00 34.84 2.69
2692 2808 3.066621 GTCAAATGGTGAAGTTGCAGACA 59.933 43.478 0.00 0.00 38.23 3.41
2727 2844 0.953960 CCCGCATATTTAGTCCCCGC 60.954 60.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.727123 TCCAGAACTTGTTGCCTCAA 57.273 45.000 0.00 0.00 0.00 3.02
44 45 5.591099 TCATTCTTTTCCAGAACTTGTTGC 58.409 37.500 0.00 0.00 44.70 4.17
82 83 3.170791 TCCTTTCGCATCTAGCTCTTG 57.829 47.619 0.00 0.00 42.61 3.02
83 84 3.494048 CCATCCTTTCGCATCTAGCTCTT 60.494 47.826 0.00 0.00 42.61 2.85
149 201 9.662947 ATTCCTACAAACATACAACTACTAACC 57.337 33.333 0.00 0.00 0.00 2.85
288 341 5.392767 TTGCCAAACAAACTGTGAAGTTA 57.607 34.783 0.00 0.00 34.56 2.24
629 686 1.284785 GGAGATGGGTTTGTGATGGGA 59.715 52.381 0.00 0.00 0.00 4.37
634 691 0.991920 GGAGGGAGATGGGTTTGTGA 59.008 55.000 0.00 0.00 0.00 3.58
638 695 0.921256 CAGGGGAGGGAGATGGGTTT 60.921 60.000 0.00 0.00 0.00 3.27
723 796 0.884259 TGCAGTGATCAACCACCACG 60.884 55.000 0.00 0.00 37.76 4.94
784 859 2.269241 CACGGAAGGAGGAAGGGC 59.731 66.667 0.00 0.00 0.00 5.19
798 873 1.191647 GAAACTACCACAAGACGCACG 59.808 52.381 0.00 0.00 0.00 5.34
817 892 0.035725 CAACCAGCAGCAGGAGATGA 60.036 55.000 11.55 0.00 31.30 2.92
854 931 7.081976 CCTAAAACCACAAATTTTCCTACTCG 58.918 38.462 0.00 0.00 31.79 4.18
880 958 8.625651 TCCAAAATTATCTCACAAACGAAAAGA 58.374 29.630 0.00 0.00 0.00 2.52
886 964 8.741101 TCAAATCCAAAATTATCTCACAAACG 57.259 30.769 0.00 0.00 0.00 3.60
924 1002 5.306937 TCAATGGGGATACAACTCATACGAT 59.693 40.000 0.00 0.00 39.74 3.73
928 1006 8.837099 AAAAATCAATGGGGATACAACTCATA 57.163 30.769 0.00 0.00 39.74 2.15
970 1049 2.029110 CACAAACCCTAACCTGCATTGG 60.029 50.000 0.00 0.00 0.00 3.16
1086 1165 4.070716 CCATCTCTAACATTGCCTCATCC 58.929 47.826 0.00 0.00 0.00 3.51
1100 1179 7.159322 GACAACTTGTCTCTTACCATCTCTA 57.841 40.000 13.77 0.00 43.73 2.43
1151 1230 8.010733 ACTTTCTTTGAAAGGAACATGATCAA 57.989 30.769 19.86 0.00 0.00 2.57
1318 1397 5.618056 TCACTTGCACTTTCATCATCTTC 57.382 39.130 0.00 0.00 0.00 2.87
1355 1434 4.037208 CCTCATTTCCCATCTCATTTTCGG 59.963 45.833 0.00 0.00 0.00 4.30
1397 1476 5.163581 GCAGTTATGATTGCATCTGGTTCTT 60.164 40.000 0.00 0.00 38.30 2.52
1561 1640 4.543689 TGTCCCTGTACCTCTATGTTAGG 58.456 47.826 0.00 0.00 40.20 2.69
1666 1769 6.829811 TGATGGATAATTTGTTGATGAGCTGA 59.170 34.615 0.00 0.00 0.00 4.26
1679 1782 8.185506 TGCATGATTTAGCTGATGGATAATTT 57.814 30.769 0.00 0.00 0.00 1.82
1696 1799 2.963101 CCTCATGTTCCCATGCATGATT 59.037 45.455 28.31 2.97 46.79 2.57
1706 1809 0.753111 GCCATCACCCTCATGTTCCC 60.753 60.000 0.00 0.00 0.00 3.97
1763 1866 3.877559 TCACTTCCTGCCACATAATCAG 58.122 45.455 0.00 0.00 0.00 2.90
2124 2235 1.946768 CTCCTTGGCGTTGAAGACAAA 59.053 47.619 0.00 0.00 38.87 2.83
2128 2239 1.000955 GACTCTCCTTGGCGTTGAAGA 59.999 52.381 0.00 0.00 0.00 2.87
2133 2244 1.201429 ATGGGACTCTCCTTGGCGTT 61.201 55.000 0.00 0.00 36.57 4.84
2155 2266 0.597072 GAAGACTTCGTCCCGTGTCT 59.403 55.000 0.00 8.38 40.63 3.41
2195 2306 6.711277 ACTATATACGTGGTCCGGACTATTA 58.289 40.000 32.52 21.55 42.24 0.98
2198 2309 4.563580 GGACTATATACGTGGTCCGGACTA 60.564 50.000 32.52 25.88 42.24 2.59
2252 2364 1.684734 GTTCGGGGGCTACTGAGGA 60.685 63.158 0.00 0.00 0.00 3.71
2278 2390 1.209275 CGCCGGACTCATCGTCATTC 61.209 60.000 5.05 0.00 44.68 2.67
2398 2512 0.036732 TGAAGGTGCAGAAGCCGATT 59.963 50.000 0.00 0.00 41.13 3.34
2520 2636 5.279406 GGAGATGGTGTGGATTAGATCTGAG 60.279 48.000 5.18 0.00 0.00 3.35
2675 2791 2.224606 CTGTGTCTGCAACTTCACCAT 58.775 47.619 0.00 0.00 0.00 3.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.